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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ), 'gf_id' => 'HOM05D001108', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001108' ), 'data_identifier' => 'HOM05D001108', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001108', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p39900' => 'bna', 'A07p00070' => 'bna', 'A10p10910' => 'bna', 'Aa31LG1G23160' => 'aar', 'Aa31LG1G23200' => 'aar', 'Aa31LG3G9630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.400' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.459' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5414' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4554' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1021' => 'aag', 'Actinidia11036' => 'ach', 'Actinidia11560' => 'ach', 'Actinidia29083' => 'ach', 'Ah.01g015170' => 'amhyb', 'Ah.02g115530' => 'amhyb', 'Ah.02g115570' => 'amhyb', 'Ah.04g164360' => 'amhyb', 'Ah.07g205420' => 'amhyb', 'Ah.13g070420' => 'amhyb', 'AL3G19950' => 'aly', 'AL3G19960' => 'aly', 'AL3G53780' => 'aly', 'AL8G28180' => 'aly', 'Aqoxy1G01439' => 'aox', 'Aqoxy1G02436' => 'aox', 'Aqoxy1G02437' => 'aox', 'Aqoxy2G00131' => 'aox', 'Aqoxy2G00133' => 'aox', 'Aqoxy5G04284' => 'aox', 'Aqoxy5G04306' => 'aox', 'Aqoxy6G01650' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0YC2K0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4S3PH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85LIYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EZRH7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IA3QS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PPEG78' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QE5WJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S0UG05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SGC5R3' => 'arhy', 'AT2G20690' => 'ath', 'AT3G08947' => 'ath', 'AT5G53480' => 'ath', 'ATR0565G001' => 'atr', 'ATR0730G036' => 'atr', 'ATR0730G211' => 'atr', 'ATR1096G056' => 'atr', 'Atru.chr12.2249' => 'acertr', 'Atru.chr6.2997' => 'acertr', 'Atru.chr8.2299' => 'acertr', 'Atru.chr8.2300' => 'acertr', 'Atru.chr8.2301' => 'acertr', 'Atru.chr9.1952' => 'acertr', 'AUR62002952' => 'cqu', 'AUR62006069' => 'cqu', 'AUR62007757' => 'cqu', 'AUR62019549' => 'cqu', 'AUR62030508' => 'cqu', 'AUR62030785' => 'cqu', 'AUR62035557' => 'cqu', 'AUR62036092' => 'cqu', 'BcaB03g16863' => 'bca', 'BcaB06g25972' => 'bca', 'BcaB06g25973' => 'bca', 'BcaB08g35711' => 'bca', 'BcaC01g04207' => 'bca', 'BcaC04g22783' => 'bca', 'BcaC05g29628' => 'bca', 'BcaC05g29736' => 'bca', 'BcaC05g29855' => 'bca', 'BcaC05g29856' => 'bca', 'BcaC06g36761' => 'bca', 'BolC5t33334H' => 'bol', 'BolC5t34547H' => 'bol', 'BolC5t34657H' => 'bol', 'BolC7t40471H' => 'bol', 'BolC9t54441H' => 'bol', 'BolC9t56339H' => 'bol', 'BolC9t57212H' => 'bol', 'BraA05t22821Z' => 'bra', 'BraA07t27798Z' => 'bra', 'BraA10t43180Z' => 'bra', 'BraSC256t45934Z' => 'bra', 'C05p46070' => 'bna', 'C05p46080' => 'bna', 'C05p58940' => 'bna', 'C05p60020' => 'bna', 'C05p60040' => 'bna', 'C07p00210' => 'bna', 'C09p15330' => 'bna', 'C09p34920' => 'bna', 'C09p34930' => 'bna', 'C09p43300' => 'bna', 'CAN.G10322.1' => 'can', 'CAN.G15.10' => 'can', 'CAN.G248.11' => 'can', 'CAN.G248.14' => 'can', 'CAN.G248.16' => 'can', 'CAN.G248.33' => 'can', 'CAN.G312.8' => 'can', 'CAN.G362.18' => 'can', 'CAN.G481.34' => 'can', 'CAN.G851.1' => 'can', 'CANSAT21G1310' => 'cansat', 'CANSAT35G0939' => 'cansat', 'CANSAT54G0401' => 'cansat', 'CANSAT80G2295' => 'cansat', 'CANSAT80G2367' => 'cansat', 'CARHR083280' => 'chi', 'CARHR111330' => 'chi', 'CARHR217660' => 'chi', 'CARHR266610' => 'chi', 'Carub.0003s0805' => 'cru', 'Carub.0003s0806' => 'cru', 'Carub.0003s3520' => 'cru', 'Carub.0008s1364' => 'cru', 'Ca_16724_v3' => 'car', 'Ca_17456_v3' => 'car', 'Ca_20056_v3' => 'car', 'Ca_28725_v3' => 'car', 'Ca_30591_v3' => 'car', 'CBR_g21240' => 'cbr', 'CBR_g36747' => 'cbr', 'Cc02_g01310' => 'ccan', 'Cc02_g01330' => 'ccan', 'Cc02_g31190' => 'ccan', 'Cc05_g07130' => 'ccan', 'Cc06_g00970' => 'ccan', 'CDE02G0464' => 'cde', 'CDE04G0828' => 'cde', 'CDE06G0643' => 'cde', 'CDE09G0563' => 'cde', 'Cfa011963' => 'cfa', 'Cfa014613' => 'cfa', 'Cfa016211' => 'cfa', 'Cfa017142' => 'cfa', 'Cfa017147' => 'cfa', 'Cfa023228' => 'cfa', 'Cfa026241' => 'cfa', 'Ciclev10011045m.g' => 'ccl', 'Ciclev10013903m.g' => 'ccl', 'Ciclev10018814m.g' => 'ccl', 'Ciclev10023883m.g' => 'ccl', 'CiPaw.04G125800' => 'cil', 'CiPaw.11G116100' => 'cil', 'CiPaw.12G080200' => 'cil', 'ClCG01G000320' => 'cla', 'ClCG01G000340' => 'cla', 'ClCG02G017630' => 'cla', 'COL.COLO4_14485' => 'col', 'COL.COLO4_16798' => 'col', 'COL.COLO4_20425' => 'col', 'COL.COLO4_33977' => 'col', 'Cpa.g.sc120.38' => 'cpa', 'Cpa.g.sc3.105' => 'cpa', 'Cpa.g.sc34.159' => 'cpa', 'Cpa.g.sc34.160' => 'cpa', 'Cre01.g034000' => 'cre', 'Cre06.g296600' => 'cre', 'CsaV3_5G000380' => 'csa', 'CsaV3_5G000400' => 'csa', 'CsaV3_6G012940' => 'csa', 'CsaV3_6G013000' => 'csa', 'CSS0002926' => 'camsi', 'CSS0007816' => 'camsi', 'CSS0009503' => 'camsi', 'CSS0017248' => 'camsi', 'CSS0028602' => 'camsi', 'CSS0039738' => 'camsi', 'CSS0042510' => 'camsi', 'CSS0044059' => 'camsi', 'DCAR_000250' => 'dca', 'DCAR_008144' => 'dca', 'DCAR_008147' => 'dca', 'DCAR_010590' => 'dca', 'DCAR_013007' => 'dca', 'DCAR_014549' => 'dca', 'DCAR_023947' => 'dca', 'DCAR_024006' => 'dca', 'Dinv08442' => 'din', 'Dinv12138' => 'din', 'Dinv23643' => 'din', 'Dinv26419' => 'din', 'Dinv29261' => 'din', 'Dinv35347' => 'din', 'Duzib084G0676' => 'dzi', 'Duzib084G1392' => 'dzi', 'Duzib093G1006' => 'dzi', 'Duzib093G2012' => 'dzi', 'Duzib106G1647' => 'dzi', 'Duzib128G0360' => 'dzi', 'Duzib128G0688' => 'dzi', 'Duzib205G0514' => 'dzi', 'Duzib205G1706' => 'dzi', 'ECA233G3887' => 'eca', 'ECA233G4864' => 'eca', 'ECA236G2808' => 'eca', 'ECA246G0340' => 'eca', 'EL10Ac3g05254' => 'bvu', 'EL10Ac4g08320' => 'bvu', 'EL10Ac5g12515' => 'bvu', 'EL10Ac9g20764' => 'bvu', 'Eucgr.A00600' => 'egr', 'Eucgr.D01707' => 'egr', 'Eucgr.K01017' => 'egr', 'FAN01G1351' => 'fan', 'FAN02G0123' => 'fan', 'FAN03G2836' => 'fan', 'FAN04G2154' => 'fan', 'FAN04G2848' => 'fan', 'FAN05G0719' => 'fan', 'FAN05G0872' => 'fan', 'FAN05G0913' => 'fan', 'FAN05G1229' => 'fan', 'FAN05G3846' => 'fan', 'FAN06G3604' => 'fan', 'FAN08G0656' => 'fan', 'FAN08G2132' => 'fan', 'FAN09G0725' => 'fan', 'FAN09G4676' => 'fan', 'FAN10G2432' => 'fan', 'FAN10G4085' => 'fan', 'FAN13G0411' => 'fan', 'FAN14G4655' => 'fan', 'FAN18G0046' => 'fan', 'FAN18G0425' => 'fan', 'FAN18G0689' => 'fan', 'FvH4_5g11510' => 'fve', 'FvH4_5g33380' => 'fve', 'FvH4_6g10890' => 'fve', 'FvH4_6g10970' => 'fve', 'FvH4_7g32050' => 'fve', 'Glyma.04G233700' => 'gma', 'Glyma.05G219300' => 'gma', 'Glyma.06G131100' => 'gma', 'Glyma.08G025600' => 'gma', 'Glyma.12G112900' => 'gma', 'Gohir.A04G094700' => 'ghi', 'Gohir.A09G128300' => 'ghi', 'Gohir.A09G185100' => 'ghi', 'Gohir.A09G185200' => 'ghi', 'Gohir.A12G248400' => 'ghi', 'Gohir.A12G248500' => 'ghi', 'Gohir.D04G134400' => 'ghi', 'Gohir.D09G124300' => 'ghi', 'Gohir.D09G180000' => 'ghi', 'Gohir.D09G180100' => 'ghi', 'Gohir.D12G249200' => 'ghi', 'Gohir.D12G249300' => 'ghi', 'Gorai.006G143100' => 'gra', 'Gorai.006G202000' => 'gra', 'Gorai.006G202100' => 'gra', 'Gorai.008G267300' => 'gra', 'Gorai.008G267400' => 'gra', 'Gorai.012G117900' => 'gra', 'GSVIVG01030311001' => 'vvi', 'GSVIVG01038575001' => 'vvi', 'HanXRQChr02g0038791' => 'han', 'HanXRQChr02g0039801' => 'han', 'HanXRQChr04g0096101' => 'han', 'HanXRQChr04g0096111' => 'han', 'HanXRQChr04g0111491' => 'han', 'HanXRQChr06g0169711' => 'han', 'HanXRQChr06g0169731' => 'han', 'HanXRQChr06g0171311' => 'han', 'HanXRQChr06g0171321' => 'han', 'HanXRQChr06g0181481' => 'han', 'HanXRQChr06g0181491' => 'han', 'HanXRQChr08g0225111' => 'han', 'HanXRQChr09g0275311' => 'han', 'HanXRQChr17g0553281' => 'han', 'HanXRQChr17g0553291' => 'han', 'HanXRQChr17g0553301' => 'han', 'Haze_00234' => 'cav', 'Haze_09118' => 'cav', 'Haze_13157' => 'cav', 'Haze_21052' => 'cav', 'Hma1.2p1_0501F.1_g167590' => 'hma', 'Hma1.2p1_0591F.1_g185210' => 'hma', 'Hma1.2p1_2994F.1_g331380' => 'hma', 'HPP92_003131' => 'vpl', 'HPP92_006334' => 'vpl', 'HPP92_012022' => 'vpl', 'HPP92_012025' => 'vpl', 'HPP92_025105' => 'vpl', 'HPP92_027870' => 'vpl', 'HPP92_027871' => 'vpl', 'Hund07929' => 'sun', 'Hund10948' => 'sun', 'Hund11643' => 'sun', 'Hund21014' => 'sun', 'Lalb_Chr03g0029441' => 'lal', 'Lalb_Chr05g0223931' => 'lal', 'Lalb_Chr09g0332141' => 'lal', 'Lalb_Chr16g0390741' => 'lal', 'Lj1g0002117' => 'lja', 'Lj1P722T15' => 'lonja', 'Lj2C69T17' => 'lonja', 'Lj3A899T65' => 'lonja', 'Lj3C948T5' => 'lonja', 'Lj3g0011439' => 'lja', 'Lj3P898T14' => 'lonja', 'Lj4g0013757' => 'lja', 'Lsat_1_v5_gn_0_44640' => 'lsa', 'Lsat_1_v5_gn_3_37280' => 'lsa', 'Lsat_1_v5_gn_4_158501' => 'lsa', 'Lsat_1_v5_gn_4_158521' => 'lsa', 'Lsat_1_v5_gn_4_42240' => 'lsa', 'Lsat_1_v5_gn_4_70021' => 'lsa', 'Lsat_1_v5_gn_5_4220' => 'lsa', 'Lsat_1_v5_gn_6_118221' => 'lsa', 'Lsat_1_v5_gn_8_101881' => 'lsa', 'Lsat_1_v5_gn_8_150060' => 'lsa', 'Lsat_1_v5_gn_9_49160' => 'lsa', 'Manes.01G040200' => 'mes', 'Manes.01G040400' => 'mes', 'Manes.05G191500' => 'mes', 'Manes.08G095300' => 'mes', 'Manes.09G109600' => 'mes', 'Manes.13G146800' => 'mes', 'Mapoly0016s0170' => 'mpo', 'Mapoly0026s0114' => 'mpo', 'MBI03_g21446_MAGBIO' => 'mbi', 'MBI06_g06479_MAGBIO' => 'mbi', 'MBI06_g06486_MAGBIO' => 'mbi', 'MBI07_g12795_MAGBIO' => 'mbi', 'MBI15_g25685_MAGBIO' => 'mbi', 'MCO11G757' => 'mco', 'MCO16G022' => 'mco', 'MD01G1223400' => 'mdo', 'MD04G1163100' => 'mdo', 'MD06G1112600' => 'mdo', 'MD07G1294100' => 'mdo', 'MD09G1247800' => 'mdo', 'MD09G1265300' => 'mdo', 'MD12G1176600' => 'mdo', 'MD14G1134000' => 'mdo', 'MD17G1240700' => 'mdo', 'Medtr0004s0220' => 'mtr', 'Medtr1g059590' => 'mtr', 'Medtr1g066930' => 'mtr', 'Medtr3g491840' => 'mtr', 'Medtr3g491860' => 'mtr', 'Medtr4g063470' => 'mtr', 'Medtr8g099785' => 'mtr', 'MELO3C000249.2' => 'cme', 'MELO3C000453.2' => 'cme', 'MELO3C000760.2' => 'cme', 'MELO3C005893.2' => 'cme', 'MELO3C005895.2' => 'cme', 'Migut.C01348' => 'egut', 'Migut.E01063' => 'egut', 'Migut.E01066' => 'egut', 'Migut.F00195' => 'egut', 'Migut.F01017' => 'egut', 'Migut.J00122' => 'egut', 'Migut.O00523' => 'egut', 'MSTRG.27015' => 'ama', 'MSTRG.5556' => 'ama', 'MSTRG.5628' => 'ama', 'MSTRG.5729' => 'ama', 'MSTRG.8642' => 'ama', 'Nitab4.5_0000015g0270' => 'nta', 'Nitab4.5_0000444g0220' => 'nta', 'Nitab4.5_0000512g0050' => 'nta', 'Nitab4.5_0000548g0020' => 'nta', 'Nitab4.5_0001570g0020' => 'nta', 'Nitab4.5_0001717g0020' => 'nta', 'Nitab4.5_0002024g0030' => 'nta', 'Nitab4.5_0004071g0020' => 'nta', 'Nitab4.5_0005335g0010' => 'nta', 'Nitab4.5_0009553g0010' => 'nta', 'Nitab4.5_0014900g0010' => 'nta', 'Nn1g04079' => 'nnu', 'Nn1g06569' => 'nnu', 'Nn3g18954' => 'nnu', 'Nn5g27571' => 'nnu', 'Oeu010696.3' => 'oeu', 'Oeu027338.1' => 'oeu', 'Oeu037048.1' => 'oeu', 'Oeu041071.1' => 'oeu', 'Oeu057629.1' => 'oeu', 'Oeu061000.1' => 'oeu', 'Oeu061001.1' => 'oeu', 'Os03g0294600' => 'osa', 'Os05g0353400' => 'osa', 'Os12g0541000' => 'osa', 'Peaxi162Scf00075g00013' => 'pax', 'Peaxi162Scf00264g00511' => 'pax', 'Peaxi162Scf00618g00037' => 'pax', 'Peaxi162Scf00618g00316' => 'pax', 'Peaxi162Scf00740g00229' => 'pax', 'Peaxi162Scf01132g00335' => 'pax', 'PGR031G1739' => 'pgr', 'PGR031G3730' => 'pgr', 'PGR142G4253' => 'pgr', 'PGSC0003DMG400018350' => 'stu', 'PGSC0003DMG400018525' => 'stu', 'PGSC0003DMG400019597' => 'stu', 'PGSC0003DMG400026641' => 'stu', 'Phvul.002G301300' => 'pvu', 'Phvul.009G050600' => 'pvu', 'Phvul.011G114100' => 'pvu', 'Potri.006G103300' => 'ptr', 'Potri.012G017500' => 'ptr', 'Potri.013G131800' => 'ptr', 'Potri.015G010400' => 'ptr', 'Potri.016G123600' => 'ptr', 'Potri.019G100500' => 'ptr', 'Pp3c11_26710' => 'ppa', 'Pp3c2_19260' => 'ppa', 'Pp3c7_5160' => 'ppa', 'PRCOL_00000785' => 'pco', 'PRCOL_00001102' => 'pco', 'Prupe.2G313900' => 'ppe', 'Prupe.3G137500' => 'ppe', 'Prupe.5G125800' => 'ppe', 'Prupe.6G282600' => 'ppe', 'Psat0s4722g0080' => 'psa', 'Psat0s4854g0040' => 'psa', 'Psat0s773g0040' => 'psa', 'Psat1g107320' => 'psa', 'Psat4g001880' => 'psa', 'Psat5g075760' => 'psa', 'Psat5g098840' => 'psa', 'Psat5g103320' => 'psa', 'PSO017G5632' => 'pso', 'PSO349G0295' => 'pso', 'PSO478G1555' => 'pso', 'PSO502G0025' => 'pso', 'PSO541G4613' => 'pso', 'PSO675G2801' => 'pso', 'PSO675G3815' => 'pso', 'PSO782G4551' => 'pso', 'QL02p029330' => 'qlo', 'QL07p005459' => 'qlo', 'QL07p034255' => 'qlo', 'QL08p038694' => 'qlo', 'QL09p007920' => 'qlo', 'RcHm_v2.0_Chr1g0381661' => 'rch', 'RcHm_v2.0_Chr2g0153941' => 'rch', 'RcHm_v2.0_Chr3g0462121' => 'rch', 'RcHm_v2.0_Chr3g0462271' => 'rch', 'RcHm_v2.0_Chr7g0186291' => 'rch', 'RcHm_v2.0_Chr7g0232111' => 'rch', 'Rhsim03G0211000' => 'rsi', 'Rhsim05G0222900' => 'rsi', 'Rhsim06G0142500' => 'rsi', 'Rhsim06G0198200' => 'rsi', 'Sabra06G0079900' => 'sbr', 'Sabra06G0080100' => 'sbr', 'Sabra12G0015000' => 'sbr', 'Sabra13G0111300' => 'sbr', 'Sabra15G0008500' => 'sbr', 'Sabra16G0118200' => 'sbr', 'Sabra16G0118400' => 'sbr', 'Sabra19G0110800' => 'sbr', 'Sabra19G0110900' => 'sbr', 'Sabra19G0112200' => 'sbr', 'SalBow1G0161' => 'sbo', 'SalBow2G2478' => 'sbo', 'SalBow4G1750' => 'sbo', 'SalBow4G2365' => 'sbo', 'SalBow4G2586' => 'sbo', 'SalBow5G0005' => 'sbo', 'Sc13g0010010' => 'sci', 'Sc21g0002830' => 'sci', 'Sc22g0002620' => 'sci', 'Sed0006363' => 'sed', 'Sed0006413' => 'sed', 'Sed0011668' => 'sed', 'Sed0013227' => 'sed', 'Sed0027572' => 'sed', 'SEGI_03983' => 'sgi', 'SEGI_10469' => 'sgi', 'SEGI_26411' => 'sgi', 'SGA_v2.0_scaffold13G06543' => 'sas', 'SGA_v2.0_scaffold154G37103' => 'sas', 'SGA_v2.0_scaffold192G40525' => 'sas', 'SGA_v2.0_scaffold25G10790' => 'sas', 'SGA_v2.0_scaffold55G19788' => 'sas', 'SGA_v2.0_scaffold92G28314' => 'sas', 'SHI02352' => 'shi', 'SHI12862' => 'shi', 'SMO137G0361' => 'smo', 'SMO245G0025' => 'smo', 'SMO301G0072' => 'smo', 'SMO301G0082' => 'smo', 'Solyc03g082940.3' => 'sly', 'Solyc06g052030.3' => 'sly', 'Solyc07g054190.4' => 'sly', 'Solyc09g005010.4' => 'sly', 'Sopen03g022750' => 'spe', 'Sopen06g018080' => 'spe', 'Sopen07g028120' => 'spe', 'Sopen09g001020' => 'spe', 'Sp3g07340' => 'spa', 'Sp3g07360' => 'spa', 'Sp3g33940' => 'spa', 'Sp6g15610' => 'spa', 'SpUn0909_0010' => 'spa', 'SpUn0909_0020' => 'spa', 'TAR369G0635' => 'tar', 'TAR374G1341' => 'tar', 'TAR375G0138' => 'tar', 'TAR623G0556' => 'tar', 'TAR627G0387' => 'tar', 'TAR629G1774' => 'tar', 'TAR633G1035' => 'tar', 'TAR636G2439' => 'tar', 'TAR636G2956' => 'tar', 'THA.LOC104811908' => 'tha', 'THA.LOC104823298' => 'tha', 'THA.LOC104824701' => 'tha', 'Thecc.03G201600' => 'tca', 'Thecc.03G201700' => 'tca', 'Thecc.05G009600' => 'tca', 'Thecc.05G172000' => 'tca', 'Thhalv10002078m.g' => 'esa', 'Thhalv10012652m.g' => 'esa', 'Thhalv10020035m.g' => 'esa', 'Thhalv10020036m.g' => 'esa', 'TPR.G17295' => 'tpr', 'TPR.G18783' => 'tpr', 'TPR.G23356' => 'tpr', 'TPR.G33620' => 'tpr', 'TPR.G33646' => 'tpr', 'TPR.G3455' => 'tpr', 'TWI15G0589' => 'twi', 'TWI60G1621' => 'twi', 'TWI74G0418' => 'twi', 'TWI75G0959' => 'twi', 'TWI77G0017' => 'twi', 'TWI81G0337' => 'twi', 'unitig_60.g25406' => 'ugi', 'unitig_88.g27586' => 'ugi', 'unitig_88.g27587' => 'ugi', 'vmacro06399' => 'vma', 'vmacro12300' => 'vma', 'vmacro20311' => 'vma', 'VMungo0251G0461' => 'vmu', 'VMungo1127G1775' => 'vmu', 'VMungo1309G1871' => 'vmu', 'Zm00001eb029010' => 'zma', 'Zm00001eb136540' => 'zma', 'Zm00001eb286470' => 'zma', 'Zm00001eb345670' => 'zma', 'Zm00001eb351190' => 'zma', 'Zm00001eb410210' => 'zma', 'Zm00001eb410410' => 'zma' ) $gf_id = 'HOM05D001108' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001108' ) $data_identifier = 'HOM05D001108' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 8, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 4, 'can' => (int) 10, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 5, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 16, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 11, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 5, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 10, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 9, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410410' $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